Re: [AMBER] the problem of charge

From: FyD <>
Date: Sun, 29 Apr 2012 12:52:45 +0200

Cao Yang,

About DPPC see
The authors have used R.E.D.

regards, Francois

Quoting FyD <>:

> Dear Cao Yang,
>> I am a user of AMBER in China. My system is a protein complex with
>> phospholipid membranes. The particial charge of DPPC is calculated
> MEP are computed using a QM program and charges are usually derived
> from the MEP during an additional fitting step (using for instance the
> RESP program). Indeed, even if the QM program provides with the MEP a
> set of charge values (ESP) they are generally not suitable for MD
> simulations as they are not equivalenced (chemical equivalencing for
> chemical equivalent atoms lead to identical charge values for atoms
> that are chemically equivalent: this is achieved during the fitting
> stage(s) by using specific charge constraints).
>> The charge of my ligand is calculated in AMBER with AM1.
>> I load the pdb file into tleap and find the whole charge of my
>> system is +5.6. So I add 6 Cl- which change the charge to -0.4
>> rather than zero. I wonder why the total charge is not zero. So My
>> question is:
>> Whether the charge equaling -0.4 be resonable in MD simulation? If
>> not, how should I make the system neutral?
>> Thanks for your time!
> - The total charge of a whole molecule such as DPPC should be an
> integer value.
> - If you generated a molecular fragment from the DPPC molecule one
> could imagine a non-integer charge value for a molecular fragment, but
> in this case the sum of the total charges of the different molecular
> fragments constructed should lead to an integer charge value.
> You can find two examples of lipids in R.E.DD.B. This corresponds to
> the work of S. Abel. See:
> In F-92, dodecylphosphocholine (DPC) is constructed from 3 elementary
> building blocks... This is quite simple to adapt this approach to the
> DPPC case.
> You might also look for in the literature for already available parameters...
> regards, Francois

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Received on Sun Apr 29 2012 - 04:00:03 PDT
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